plot_phi_marginal {BEDASSLE}  R Documentation 
Plots the posterior marginal density of a phi parameter. Users may specify whether
they want a histogram, a density, or both. For convenience, the F_{k}
statistic is presented in place of the phi parameter, as this is the statistic users
care about. F_{k}
is defined as \frac{1}{1+phi_{k}}
.
plot_phi_marginal(phi, percent.burnin = 0, thinning = 1, population.names = NULL,
pop.index = NULL,histogram = TRUE, density = TRUE)
phi 
The vector of phi values estimated for a single population from an MCMC run. 
percent.burnin 
The percent of the sampled MCMC generations to be discarded as "burnin." If the
MCMC is run for 1,000,000 generations, and sampled every 1,000 generations, there
will be 1,000 sampled generations. A 
thinning 
The multiple by which the sampled MCMC generations are thinned. A 
population.names 
The name of the population/individual for which the marginal density of the phi
parameter is being plotted. This will be used to title the marginal plot. If

pop.index 
A population index number generated to title a marginal plot if no

histogram 
A switch that controls whether or not the plot contains a histogram of the values
estimated for the parameter over the course of the MCMC. Default is 
density 
A switch that controls whether or not the plot shows the density of the values
estimated for the parameter over the course of the MCMC. Default is 
The marginal plot is another basic visual tool for MCMC diagnosis. Users should look for marginal plots that are "smooth as eggs" (indicating that the chain has been run long enough) and unimodal (indicating a single peak in the likelihood surface).
Gideon Bradburd